tbuckley/cabot-search huggingface dataset:
BIOM-18. MOLECULAR FEATURES RELATED TO LONG-TERM SURVIVAL IN GLIOBLASTOMA
Authors: Michal Nisnboym, Itay Raphael, Jan Drappatz
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond 2years of survival despite multimodal treatment. Strikingly, small fractions of GBM patients seem to display extended survival. However, the underlying mechanisms for this peculiarity remain largely unknown. Long-term survival (LTS) is often defined as a survival time of more than 3-5years from diagnosis. Several clinical variables have been associated with patients' survival, with age, Karnofsky performance score (KPS), and extent of resection being the most consistent. With advances in multi-omics technologies and their integration with disease diagnostics, numerous prognostic molecular markers have been proposed. So far, only O6-methylguanine-DNA-methyltransferase (MGMT) gene promotor hypermethylation is a well-established biomarker that is linked to outcome and therapy response. The objective of this study is to revisit patients diagnosed with GBM according to the 2021 WHO classification and investigate molecular characteristics associated with LTS. We analyzed records of IDH-wildtype GBM patients, &amp;gt; 18 years old, operated and treated at our institution between 2013 and 2020. From a patient perspective, we defined long-term survivorship as patients surviving more than 5 years. We compared LTSs to an equal number of matched controls (by clinical features and MGMT status) with STS, surviving less than 18 months. The analysis of their molecular features was performed by using the well-established and commonly used next-generation sequencing (NGS) assay, Glioseq. RESULTS: will be presented. With this retrospective work, we hope to shed a broader light on the still unknown molecular features as possible mechanisms behind the LTS of GBM patients. This is to pave the way for a consolidated conclusion on this important topic.
PATH-54. CDC42BPA::BRAF REPRESENTS A NOVEL FUSION IN DESMOPLASTIC INFANTILE GLIOMA
Authors: Maria Isabel Barros Guinle, Ella A Nettnin, Emon Nasajpour, Jeffrey Nirschl, Cesar A Garcia, Hannes Vogel, Kristen Yeom, Laura Prolo, Claudia Petritsch
Journal: Neuro-Oncology (2023)

Abstract Desmoplastic infantile ganglioglioma/desmoplastic infantile astrocytomas (DIG/DIA), although rare, are low-grade glioneuronal tumors that typically affect patients &amp;lt; 1 year old, and generally carry a good prognosis. Often successfully cured with surgical excision, DIG/DIA still carry the potential for malignant transformation or recurrence. Whilst pediatric low grade glioma (LGG) survival rates are &amp;gt;95%, tumor grade does not correlate well with outcomes in infant LGG (iLGG), thus highlighting the need for investigation into molecular mechanisms of tumor progression. We describe a novel CDC42BPA-BRAF fusion in a DIA in a three-month old patient, and its detection via Next Generation Sequencing. Future studies will investigate whether this novel fusion can function as a target for BRAF and MAPK pathway inhibitors, which have recently been FDA-approved for pLGG.
STEM-18. HYPOXIA-REGULATED EXPRESSION OF CD44 AND OSTEOPONTIN CAN CHANGE THE PHENOTYPE OF GLIOMA STEM-LIKE CELLS FROM HIGHLY INVASIVE TO LESS INVASIVE/PROLIFERATIVE TUMORS IN GLIOBLASTOMA
Authors: Masahiro Nishikawa, Akihiro Inoue, Takanori Ohnishi, Saya Ozaki, Yonehiro Kanemura, Satoshi Suehiro, Shohei Kohno, Shiro Ohue, Seiji Shigekawa, Hideaki Watanabe, Takeharu Kunieda
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The poor prognosis of glioblastoma multiforme (GBM) is primarily due to highly invasive and highly migratory glioma stem-like cells(GSCs) in tumors. Upon GBM recurrence or progression, the highly invasive phenotype of GSCs changes to a less-motile, proliferative phenotype, thus generating tumor mass. Elucidating the molecular mechanism underlying this phenotypic transition could lead to the identification of effective molecular targets for treating GBM. METHODS We examined the effects of hypoxia (1% O2: severe or 5% O2: moderate) on the expression and functions of hypoxia-inducible factor(HIF), CD44 and osteopontin (OPN) to clarify the role of these molecules in GBM tumor invasion and proliferation. We also investigated the anti-tumor effects of CD44 knockdown in vitro and in vivo using a GSC-transplantation mouse model. RESULTS Severe Hypoxia upregulates CD44 expression via activation of HIF-1α, inducing GSCs to assume a highly invasive phenotype. In contrast, moderate hypoxia upregulates OPN expression via activation of HIF-2α. OPN inhibits CD44-promoted GSC migration and invasion and stimulates GSC proliferation, resulting in GSCs assuming a less-invasive, highly proliferative phenotype. CD44 knockdown significantly inhibited GSC migration and invasion both in vitro and in vivo, and the mice survived significantly longer than control mice. CONCLUSION The highly invasive phenotype of GSCs can be reversed by switching from severe to moderate hypoxia, leading to less-invasive and proliferative tumors. CD44 and OPN play a central role in regulating GSC invasion and proliferation by inducing a phenotypic transition, suggesting that these molecules could be effective targets for treating GBM.
CTNI-07. PHASE I STUDY OF PAXALISIB AND RADIOTHERAPY FOR CNS DISEASE HARBORING PI3K PATHWAY MUTATIONS: PILOT ANALYSIS OF CIRCULATING TUMOR DNA FOR PATIENT ELIGIBILITY CONFIRMATION AND POST-TREATMENT RESPONSE
Authors: Brandon Imber, Vignesh Ravichandran, Pavitra Rao, Hilary Casanova, John Friend, Jeremy Simpson, Luke Pike, Melissa Zinovoy, Ryan Mitchell, Christina Chacko, Rupesh Kotecha, Somica Somai, Adrienne Boire, Igor Gavrilovic, Anna Piotrowski, Jessica Wilcox, Rachna Malani, Robert Young, Michael Offin, Eli Diamond, Jonathan Yang
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Radiotherapy (RT) is effective for brain metastases (BM) or leptomeningeal disease (LMD), but disease control is poor for tumors harboring PI3K pathway alterations (PI3Kalt). We hypothesized that combining RT with paxalisib, a CNS-penetrant PI3K/mTOR inhibitor, offers therapeutic synergy. The role of plasma circulating tumor DNA (ctDNA) to confirm study eligibility and response monitoring is unclear. METHODS This is a multi-institutional, phase I trial of concurrent paxalisib and whole brain RT (30 Gy in 10 fractions, NCT04192981) for CNS disease. To establish eligibility, patients had documented PI3Kalt performed using institutional tumor targeted sequencing (MSK-IMPACT) of primary or metastatic tumors (eligibility sequencing). Plasma ctDNA was collected at baseline and 3-, 6- and 9-months post-treatment and sequenced using institutional plasma ctDNA targeted sequencing platform (MSK-ACCESS). Our objectives were to a) determine PI3Kalt concordance between eligibility sequencing and baseline ctDNA and b) analyze quantitative post-treatment plasma ctDNA dynamics. RESULTS Between 3/2020-5/2023, 15 patients were enrolled to receive daily paxalisib (45mg, n = 11 or 60mg, n = 4) and WBRT. Twelve were treated for BM and 3 for LMD. Eligibility sequencing was determined a median of 8.1months (range: 2.4-38.6) pre-study enrollment and the most common PI3Kalt were PIK3CA (n = 7), INPP4B (n = 2), INPPL1 (n = 1) and PIK3CG (n = 1), and PTEN copy number alterations (homdel n = 2). Baseline ctDNA was sequenced from 13/15 patients (18 samples: baseline = 13, 3-months = 4 and 6-months = 1). We confirmed 100% of PIK3CA mutations using baseline ctDNA. One breast cancer BM patient demonstrated significant variant allele frequency reduction from 50% (baseline) to 0.1% (3-months post-treatment) for two tracked PIK3CA mutations (p.E545K and p.A1066V), which correlated with a partial response per RANO-BM. CONCLUSIONS For patients on genomically-driven targeted therapy and RT combination trials, alterations detected using plasma ctDNA, especially PIK3CA, may be used to rapidly assess eligibility. Serial ctDNA collection may serve as a potential response biomarker with further validation.
CTNI-70. RADIOTHERAPY QUALITY ASSURANCE IN THE ROAM/EORTC1308 ATYPICAL MENINGIOMA RANDOMISED CONTROLLED TRIAL: PROSPECTIVE REVIEW IMPROVES RADIOTHERAPY QUALITY AND CONSISTENCY
Authors: Michael Jenkinson, Helen Mayles, Damien Weber, Brian Haylock
Journal: Neuro-Oncology (2023)

Abstract OBJECTIVE ROAM/1308 is an international randomised controlled phase III trial comparing radiotherapy (60Gy in 30 fractions) to observation following complete surgical resection of atypical meningioma. We embedded prospective radiotherapy quality assurance (RTQA) within the trial with the aim of ensuring consistent radiotherapy planning and delivery. METHODS The radiotherapy protocol described the consensus contouring/planning guidelines. Pre-trial assessment included benchmark cases (outlining/planning) and a technology ‘Dummy Run’. Individual case reviews were undertaken. Non-conformities were classed as ‘major’ (undertreatment of dural margins/over treatment of brain or organs at risk) or ‘minor’ (for education). Resubmissions were mandated for all major non-conformities. All plans were approved before radiotherapy delivery. RESULTS The UK RTQA group coordinated European sites. The Australian RTQA group (TROG) reviewed their sites and provided all data to the UK for review. Four radiation oncologists reviewed contours and physicists/dosimetrists reviewed plans. All sites (20 UK, 25 EORTC, 11 TROG) undertook the benchmark/’Dummy Run’ cases prior to opening. Resubmissions were: UK (1 contour, 0 plans), EORTC (2 contours, 6 plans) and TROG (1 contour, 3 plans). Trial communications and outlining workshops were used to provide feedback. Radiotherapy was delivered to 30, 26 and 7 patients at 11 UK, 12 EORTC and 5 TROG sites, respectively. Overall, 25 (40%) patient cases needed resubmitting: 23 (37%) sets of outlines (2 cases twice) and 9 (14%) treatment plans (1 plan twice). CONCLUSIONS Prospective quality assurance and case review are essential to ensure consistent high-quality radiotherapy and benchmark/’Dummy Run’ alone is not sufficient. RTQA should be used for future trials in rare tumours where centres may only treat a few patients. The consistent high-quality radiotherapy in ROAM/EORTC1308 ensures the primary outcome (progression free survival: to report 2026) will be a robust assessment and any difference between treatment arms cannot be attributed to variation in radiotherapy planning or delivery.
TMIC-12. RAB27 REGULATION OF VASCULAR WALL INTEGRITY MEDIATES T-CELL INFILTERATION IN GLIOBLASTOMA
Authors: Lata Adnani, Brian Meehan, Janusz Rak
Journal: Neuro-Oncology (2023)

Abstract Endothelial secretome exerts a potent influence on the phenotype of cancer cells and immune microenvironment. Recently, we have reported that glioblastoma stem cells acquire a more aggressive mesenchymal state under influence of vascular endothelial cell derived extracellular vesicles (EVs). Since Rab27, GTPases involved in multiple aspects of EV (exosome) biogenesis, has been implicated in control of angiogenic pathways through regulation of VEGFR1 turnover and possibly other mechanisms, we interrogated the role of Rab27 in the function of normal and glioblastoma associated brain microvasculature. Using mice with disrupted Rab27a and Rab27b isoforms, we documented that these proteins control development and stability of the brain vasculature including pathological angiogenesis in glioblastoma. Thus, relative to wild-type C57bl/6 (WT) and double heterozygous Rab27a+/-;Rab27b+/- (dHET) mice, animals with Rab27a/b double knock-out (Rab27a/b-dKO) exhibit reduced microvascular density in brain cortices. When neoangiogensis was induced following orthotopic inoculation of mouse glioma cells (GL261), multiple morphological anomalies were observed in the tumour vasculature relative to tumours established in control mice. Moreover, vascular permeability of tumours in Rab27a/b-dKO mice markedly exceeded that of similar tumours in wild type or heterozygous controls resulting in augmented T-cell infiltration into the otherwise ‘cold’ brain tumor microenvironment. Our results suggest that key switches in the cellular secretome, such as Rab27a and Rab27b, may impact endothelial membrane dynamic and intercellular interactions capabilities, whereby they may play a critical role in ensuring the stability and sustained cellular barrier function of the vasculature during brain tumour progression. Therapeutic implications of these findings are being explored.
BIOM-59. FEASIBILITY AND UTILITY OF THE NOVEL CANCER COMPREHENSIVE GENOMIC PROFILING RNA-SEQ FOR THE IDENTIFICATION OF THERAPEUTIC TARGETS AND DIAGNOSTIC BIOMARKERS IN GLIOMA
Authors: Masamichi Takahashi, Shinji Kohsaka, Koichi Ichimura, Hiroyuki Mano, Yoshitaka Narita
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The detection of novel therapeutic targets is increasingly important in oncology. The Todai OncoPanel (TOP) RNA panel is a custom target RNA-seq using the junction capture method to maximize the sensitivity in detecting of known 456 fusion gene transcripts, which is approved in Japan in 2022 and covered by insurance in later 2023. Above, TOP RNA panel interrogates aberrantly spliced transcripts and analyzes the expression profiles of 1,390 genes. Primary brain tumors require various molecular profiles to be classified based on WHO2021 classification and also necessitates new therapeutic targets. In this study, we aimed to classify gliomas and identify the molecular targets by TOP RNA panel. METHODS Among 131 frozen samples of malignant gliomas, 124 samples passed quality control and were subjected to TOP RNA panel. Fusion detection and RNA expression analysis were conducted with the original pipeline. Cluster analysis and Gene Set Enrichment Analysis (GSEA) were performed to identify gene sets specific for individual subtypes. Copy numbers of tyrosine kinase genes, MDM2 and CDK4 were evaluated by digital droplet PCR (ddPCR). RESULTS Among 55 cases of glioblastoma, gene fusions were detected in 11 cases (20.0%) including novel MET fusions, and overexpression of seven tyrosine kinase genes were observed in 15 cases (27.3%). Of the 34 overexpressed genes, gene amplification was observed in 17 genes (50%) by ddPCR. In contrast to IDH-wildtype glioblastoma, IDH-mutant tumors hardly harbored fusion genes or gene overexpression. GSEA identified that the gene sets related to 1p36 and 19q were relatively enriched in astrocytoma, suggesting that regional genomic DNA copy number alterations can be evaluated by gene expression analysis. CONCLUSION TOP RNA panel detects more fusions than DNA panel and is utilized not only for the detection of molecular targets but also for the molecular classification of glioma, providing treatments optimized for the individual patients.
TMIC-63. SINGLE CELL SEQUENCING OF RECURRENT GLIOBLASTOMA DEFINES CELLULAR STATES ASSOCIATED WITH THERAPY RESISTANCE
Authors: Arushi Tripathi, Sunita Shankar, Visweswaran Ravikumar, Jackson Loper, Sunjong Ji, Zainab Hassan, Yacoub Haydin, Dah-Luen Huang, Sagnik Bhadury, Jeffrey Regier, Arvind Rao, Wajd Al-holou
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM), an aggressive, primary tumor is composed of multiple clonal populations. Resistance to therapy is a hallmark of GBM, making it a deadly disease. Upon therapeutic stress, tumor heterogeneity and glial stem cell plasticity within the primary tumor contributes to reprogramming of the transcriptional activity. This alters the tumor landscape and generates therapy resistant clonal populations. Single cell RNA sequencing studies of primary GBM have defined various tumor cell states namely, the NPC-like (Neuronal precursor-like), OPC-like (oligodendrocyte precursor-like) and MES-like (mesenchymal-like) cellular states. These studies have also defined the immune components and the normal brain cells associated with primary GBM. Yet, there are no studies focused on the single cell analysis of recurrent GBM. To define the tumor landscape at recurrence, we performed single cell RNA sequencing of 180K cells from excised tumor tissue obtained from 11 patients after failure of therapeutic interventions. A corresponding cohort of 240K cells were sequenced from primary tumors obtained from 13 patients. We performed cellular state analyses of tumor cells in both the primary (~70K) and recurrent (~10K) samples. Primary GBM showed higher fractions of AC-like (0.55), compared to NPC-like (0.10), OPC-like (0.20) and MES-like (0.15). On the other hand, recurrent tissues have very low AC-like (0.09) but elevated NPC-like (0.23), OPC-like (0.40) and MES-like (0.27). This data shows a significant decrease in AC-like cells and corresponding increase in MES-like, OPC-like, NPC-like cells after recurrence. Within this dataset we also have matched longitudinal samples for analysis. We are currently performing trajectory analysis to identify genes and transcription programs activated during tumor recurrence. Experimentally, using known markers for the different cellular states we have also performed immunofluorescence analyses to validate the different cell states altered during recurrence. Our efforts to generate comprehensive recurrent GBM atlas will prove to be valuable to the GBM community.
IMMU-04. LOW-INTENSITY PULSED ULTRASOUND ENHANCES CAR T CELL THERAPY BY INDUCING TWO-WAY IMMUNE CELL TRAFFICKING – T CELL INTO TUMOR AND MYELOID CELL INTO PERIPHERY IN A SYNGENEIC MOUSE GLIOBLASTOMA MODEL
Authors: Akane Yamamichi, Tiffany Chen, Su Phyu, Jacob Young, Keith Kyewarabye, Ryusuke Hatae, Marco Gallus, Michael Canney, Adam Sonabend, Hideho Okada
Journal: Neuro-Oncology (2023)

Abstract Chimeric Antigen Receptor (CAR) T-cell therapy has been successful against hematological malignancies. However, it has not established efficacy in glioblastoma (GBM) patients. Significant challenges currently limiting the effectiveness of CAR T-cell therapy for patients with GBM include poor CAR-T cell trafficking to GBM due to the blood-brain barrier, and the presence of highly immunosuppressive and pro-tumoral tumor-associated macrophages (TAMs) in the tumor microenvironment. Furthermore, the heterogeneous expression of target antigens in GBM can lead to antigen escape and therapeutic resistance. Low-intensity pulsed ultrasound with microbubbles (LIPU/MB) has been shown to enhance CAR T-cell trafficking and improve survival in immunocompromised xenograft mice GBM models. In this study, we investigated whether multiple rounds of LIPU/MB can improve not only CAR T-cell but also endogenous T-cell infiltration into the tumors and induce myeloid cell trafficking into lymph nodes (LNs), thus enhancing CAR T-cell therapy against GBM in the immunocompetent syngeneic mice model. We recently developed a novel immunocompetent transgenic (Tg) mouse that expresses an anti-EGFRvIII CAR on T-cells and enables us to investigate the interaction between CAR T-cells and the endogenous immune environment. C57BL6/J mice bearing intracerebral EGFRvIII+ GBM received an intravenous administration of anti-EGFRvIII CAR T-cells derived from Tg-mice. The mice were stratified to receive single-LIPU (1 min before CAR T-cells administration) or triple-LIPU/MB (1 min before CAR T-cells administration, then two and four days later). Triple-LIPU/MB significantly suppressed tumor growth and improved survival and was associated with increased CAR T-cells and endogenous T-cells infiltration into the tumors compared with single-LIPU/MB or without LIPU. Furthermore, draining cervical LNs showed increased macrophages trafficking after triple-LIPU/MB. Moreover, TAMs isolated from triple-LIPU/MB mice brains showed higher levels of MHC-II expression. These results suggest that LIPU/MB may promote the tumor antigen presentation to endogenous T-cells and enhance the efficacy of CAR T-cell therapy for GBM.
STEM-09. EXPLORING THE ROLE OF <i>TP53</i> IN REDOX REGULATION AND RESPONSE OF GLIOBLASTOMA STEM CELLS TO ROS-INDUCING AGENTS
Authors: Fatemeh Jamali, Vincent April, Siham Sabri, Bassam Abdulkarim
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma, the most malignant primary tumor of the central nervous system in adults presents a major therapeutic challenge due to the presence of chemo-radioresistant glioblastoma stem cells (GSCs). These GSCs adapt the thioredoxin (Trx) and glutathione (GSH) antioxidant systems to counteract treatment-induced reactive oxygen species (ROS) and promote their survival. The tumor suppressor gene wild-type (wt)TP53 regulates the expression of pro-oxidant or antioxidant genes in response to chemoradiotherapy based on p53 DNA-binding activity in a reducing microenvironment. Given the importance of p53 as a redox-sensitive protein, we hypothesized that p53 might protect GSCs against ROS-inducing agents. Auranofin (Au), a FDA-approved gold(I)-containing compound inhibits thioredoxin reductase 1 (TrxR1), a key antioxidant protein. We investigated the effects of Au on different GSCs including wtp53 GSC line and its counterpart p53-knockdown. We assessed viability, neurosphere formation, ROS levels and expression of p53 and TrXR1 to evaluate the cytotoxicity of Au, alone and in combination with L-buthionine sulfoximine (L-BSO), a GSH-depleting agent. We conducted TCGA analysis to explore the correlation between TrxR1 and p53. Our findings revealed a positive significant correlation between p53 and TrxR1 expression, consistent with lower levels of TrxR1 in p53-knockdown GSCs compared to their wt-p53 counterparts. P53-knockdown GSCs displayed a higher basal level of ROS, which further increased upon treatment with Au. P53-knockdown significantly increased the sensitivity of cells to Au, with pronounced effects for Au/L-BSO combination. Our findings reveal that expression levels of wtp53 affect the role of p53 in TrxR1-redox regulation and sensitivity to ROS-inducing agents in GSCs.